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9qh2

wild-type APO Purine Nucleoside Phosphorylase from Parageobacillus thermoglucosidasius

Method: X-RAY DIFFRACTION D_max: 73.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qh2
deposition_date	2025-03-14
last_revision	2026-03-25
title	wild-type APO Purine Nucleoside Phosphorylase from Parageobacillus thermoglucosidasius
keywords	phosphorylase, hexameric, nucleoside catabolism, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	23.13 Å
rg_electron	22.10 Å
i0	43735300.00
molecular_weight	51596.0 kDa
excluded_volume	64703 Å³
envelope_volume	74778 Å³
shell_volume	27608 Å³
envelope_diameter	73.9 Å
shell_rg	29.54 Å
envelope_rg	22.15 Å
shape_rg	22.12 Å
total_rg	22.88 Å
total_atoms	3651
n_residues	472
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	73.5 Å
rg_real	23.01 Å
rg_real_error	0.34 Å
i0_real	4.3740e+07
i0_real_error	5.3650e+05
rg_reciprocal	23.04 Å
i0_reciprocal	43740000.0000
total_estimate	0.8929
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.3 Å
skewness	0.210
kurtosis	-0.403
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	11240000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.964

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Purine-nucleoside phosphorylase
formula_weight	27544.3 kDa
ec_number	2.4.2.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4065

MMRGSHHHHHHGSLSIHIEAKQQEIAEKILLPGDPLRAQYIAETFLEGATCYNRVRGMLGFTGTYKGHRISVQGTGMGVPSISIYVNELIQSYHVQTLIRVGTCGAIQKDVNVRDVILAMSASTDSNMNRLTFRGRDYAPTANFALLRTAYEVGAEKGLPLKVGSVFTADMFYNDEPDWETWARYGVLAVEMETAALYTLAAKFGRKALSVLTVSDHILTGEETTAQERQTTFNDMIEVALETAIRVE

Source

organism	Parageobacillus thermoglucosidasius
ncbi_taxonomy_id	1426
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	295

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6. Citations (1)

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length_a	93.662 Å
length_b	93.662 Å
length_c	94.148 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 63
int_tables_number	173
crystal_system	hexagonal

resolution	1.700 Å
resolution_low	81.110 Å
r_factor	0.1780
r_work	0.1763
r_free	0.2108

fit	/app/data/saxs_computation/qh/9qh2/9qh2.fit
pddf	/app/data/pr_computation/qh/9qh2/9qh2.pr.out
profile	/app/data/saxs_computation/qh/9qh2/9qh2.dat